Immunochemistry is a common tool in medical diagnostics and it is also usual for the assessment of therapeutic biomarkers. The latter, in particular, often require a quantitative evaluation of the extent of their presence. The application of antibodies to cells and tissues presents specific difficulties beyond those encountered when these reagents are applied to purified proteins immobilized onto solid supports in or solution. There are many factors that can affect immunodetection, among these fixation and preparation of tissue, duration and type of antigen retrieval and antibody specificity. An additional difficulty is the ability to detect targets present at low levels. In common with soluble assays, this becomes a matter of increasing signal without raising the level of nonspecific background. The approach that has been most commonly explored is signal amplification, which is achieved by successive rounds of enzymatic reactions.
DAB is a chromogeninc substrate of horse radish peroxidase (HRP) that is widely used for visualizing of target proteins in histological samples which are labeled with peroxidase activity. The method utilizes that HRP linked to antibodies targeted to proteins of a sample deposits DAB from a solution to the sites of targeted proteins and thereby labels the proteins. The method is not especially sensitive and therefore suitable for detection of relatively abundant target proteins. The signal associated with DAB deposits cannot be further amplified. Other drawbacks to mention are that the method demands rather high amounts of target specific antibodies to saturate all target sites and it is relatively slow. Furthermore, the method provides a uniform staining pattern that appears to the microscopist as a homogeneous color with intracellular resolution of cellular structures, e.g. membrane, cytoplasm, and nucleus, which makes it impossible to quantify the staining accurately.
Catalized signal amplification (CSA) (described in U.S. Pat. Nos. 5,863,748; 5,688,966; 5,767,267; 5,721,158; 5,583,001; 5,196,306; 6,372,937; 6,593,100; U.S. Pat. No. 6,593,100) adopted biotinyl- and fluorescyl-tyramide to increase the signal from HRP labeled target proteins and allowed thus detection of low abundance targets that are otherwise undetectable by the conventional method (i.e. above method). However, due to a strong background staining and difficult interpretation of the results of staining, in particular of Fluorescent in-situ hybridization (FISH) and immunohistochemistry (IHC) samples, CSA has never been widely accepted as a routine approach for evaluation of histological samples in clinical histopathology.
Recently, it has been described another HRP-based amplification method allowing detection of low abundance target molecules in IHC samples (described in WO2009036760, WO2010094283 and WO2010094284). The method utilizes DAB not as a chromogenic substrate of HRP, but as a cross-linking agent which mediates deposition of other detectable HRP substrates by HRP. The method provides for a strong amplification of a signal of the deposited HRP substrate, which makes the sensitivity of the method to be comparable with the CSA method, but compared to the latter method the new method advantageously provides no background labeling. Among other advantages of this new method it is worth to mention that the speed of the detection procedure is much faster than either the traditional DAB or biotinyl-tyramide detection procedure. However, the problem of the previous methods, namely assessment of quantity of the target in IHC samples that is based on the assessment of the quantity of detected stain, has not been solved. The new method provides a staining pattern which is very crisp, but is the same uniform staining with intracellular resolution of cellular structures as of the traditional DAB methods or CSA method. This stain pattern does not allow direct approximating the quantity of the target to the quantity of the stain in a sample, because the correlation between these two quantities is not linear. Accordingly, the quantity of a target in a histological sample visualized by all these methods can only be assessed relatively, not precisely.
Thus, whilst quality assurance schemes for the methodology have been improved and raised the standards of IHC staining, the schemes that relate to interpretation of the staining results have not been changed. Different scoring systems using varying cut-off levels for assessing whether a tissue is “positive” or “negative” are normally used for assessment of antigens. Such currently used assessment is inevitably associated with errors which may be of crucial importance in medical diagnostic.
Assessment of target expression based of evaluation of the precise quantity of individual target molecules present in samples, so called single molecule detection (SMD) approach, could be a way to a new scoring system in IHC that would be more reliable and reputable for both medical diagnostics and therapy. Unfortunately, the number of available techniques allowing visualizing single molecules of target proteins in histological samples is presently very limited and they are rather laborious and long procedures.
Basically, all the available single protein molecule detection techniques use DNA-based amplification systems Single protein molecule detection was first demonstrated with the advent of immuno-PCR (Sano T, Smith C L, Cantor C R. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 1992; 258:120-122; Adler M, Wacker R, Niemeyer C M. A real-time immuno-PCR assay for routine ultrasensitive quantification of proteins. Biochem Biophys Res Commun 2003; 308:240-250; Niemeyer C M, Adler M, Wacker R. Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification. Trends Biotechnol 2005; 23:208-216). Using antibody-DNA hybrid constructs, the antibody's binding affinity was complemented by the sensitive detection achievable with PCR. In addition, immuno-DNA detection strategies have been extended to use rolling circle amplification (RCA), an isothermal technique that generates a long ssDNA oligomer tethered to the immuno-DNA conjugate. (Gusev Y, Sparkowski J, Raghunathan A, Ferguson H Jr, Montano J, Bogdan N, Schweitzer B, Wiltshire S, Kingsmore S F, Maltzman W, Wheeler V. Rolling circle amplification: a new approach to increase sensitivity for immunohistochemistry and flow cytometry. Am J Pathol 2001; 159:63-69).
Some of the substantial drawbacks of these SMD approaches to mention are that                (i) synthesis of the antibody-DNA hybrids can be problematic as controlling the location and number of DNA conjugates per protein is not always straightforward, often leading to heterogeneous ratios of DNA tags per antibody; amplification reaction is difficult to control; amplification step is temperature sensitive; labeling is not stable-the label will defuse from the target over time; etc. Despite of recent developments in site-specific conjugation of oligonucleotide tags to proteins using intein chemistry (or chemical ligation) have been very successful, conjugate preparation still remains laborious;        (ii) steps of the methods require the temperature control;        (iii) detection procedures comprise too many steps; and        (iv) the whole process of detection takes a relatively long time.        
The SMD approach of the present invention overcomes the above obstacles and makes visualization and quantification of single entities of targets in samples wherein said single entities are immobilized simple and reliable.